BACKGROUND: Predicting protein complexes from experimental data remains a challenge due to limited resolution and stochastic errors of high-throughput methods. Current algorithms to reconstruct the complexes typically rely on a two-step process. First, they construct an interaction graph from the data, predominantly using heuristics, and subsequently cluster its vertices to identify protein complexes. RESULTS: We propose a model-based identification of protein complexes directly from the experimental observations. Our model of protein complexes based on Markov random fields explicitly incorporates false negative and false positive errors and exhibits a high robustness to noise. A model-based quality score for the resulting clusters allows us to identify reliable predictions in the complete data set. Comparisons with prior work on reference data sets shows favorable results, particularly for larger unfiltered data sets. Additional information on predictions, including the source code under the GNU Public License can be found at http://algorithmics.molgen.mpg.de/Static/Supplements/ProteinComplexes. CONCLUSION: We can identify complexes in the data obtained from high-throughput experiments without prior elimination of proteins or weak interactions. The few parameters of our model, which does not rely on heuristics, can be estimated using maximum likelihood without a reference data set. This is particularly important for protein complex studies in organisms that do not have an established reference frame of known protein complexes.

In this paper we introduce a new algorithm for image and video texture synthesis. In our approach, patch regions from a sample image or video are transformed and copied to the output and then stitched together along optimal seams to generate a new (and typically larger) output. In contrast to other techniques, the size of the patch is not chosen a-priori , but instead a graph cut technique is used to determine the optimal patch region for any given offset between the input and output texture. Unlike dynamic programming, our graph cut technique for seam optimization is applicable in any dimension. We specifically explore it in 2D and 3D to perform video texture synthesis in addition to regular image synthesis. We present approximative offset search techniques that work well in conjunction with the presented patch size optimization. We show results for synthesizing regular, random, and natural images and videos. We also demonstrate how this method can be used to interactively merge different images to generate new scenes.

We present a method to extract relative depth information from an uncalibrated monocular video sequence. Our method detects occlusions caused by an object moving in a static scene to infer relative depth relationships between scene parts. Our approach does not rely on any strong assumptions about the object or the scene to aid in this segmentation into layers. In general, the problem of building relative depth relationships from occlusion events is underconstrained, even in the absence of observation noise. A minimum description length algorithm is used to reliably calculate layer opacities and their depth relationships in the absence of hard constraints. Our approach extends previously published approaches that are restricted to work with a certain type of moving object or require strong image edges to allow for an a-priori segmentation of the scene. We also discuss ideas on how to extend our algorithm to make use of a richer set of observations.

We present techniques for rendering and animation of realistic scenes by analyzing and training on short video sequences. This work extends the new paradigm for computer animation, video tex(cid:173) tures, which uses recorded video to generate novel animations by replaying the video samples in a new order. Here we concentrate on video sprites, which are a special type of video texture. In video sprites, instead of storing whole images, the object of inter(cid:173) est is separated from the background and the video samples are stored as a sequence of alpha-matted sprites with associated veloc(cid:173) ity information. They can be rendered anywhere on the screen to create a novel animation of the object. We present methods to cre(cid:173) ate such animations by finding a sequence of sprite samples that is both visually smooth and follows a desired path. To estimate visual smoothness, we train a linear classifier to estimate visual similarity between video samples. If the motion path is known in advance, we use beam search to find a good sample sequence. We can specify the motion interactively by precomputing the sequence cost function using Q-Iearning.

This paper introduces a new type of medium, called a video texture, which has qualities somewhere between those of a photograph and a video. A video texture provides a continuous infinitely varying stream of images. While the individual frames of a video texture may be repeated from time to time, the video sequence as a whole is never repeated exactly. Video textures can be used in place of digital photos to infuse a static image with dynamic qualities and explicit actions. We present techniques for analyzing a video clip to extract its structure, and for synthesizing a new, similar looking video of arbitrary length. We combine video textures with view morphing techniques to obtain 3D video textures. We also introduce video-based animation, in which the synthesis of video textures can be guided by a user through high-level interactive controls. Applications of video textures and their extensions include the display of dynamic scenes on web pages, the creation of dynamic backdrops for special effects and games, and the interactive control of video-based animation.